# Unsolved

The problem hasn't been solved

## install rosetta problems

Hi,
I am trying install rosetta on the fedora system,with gcc 4.1.2 and scons 2.0.1. But I encountered a problem while I install with the command:scons bin mode=release.
there are two warnings that always repeat again and again, I do not know how to solve this problem.
scons: warning: The build_dir keyword has been deprecated; use the variant_dir keyword instead.
File "/xtal_programs/rosetta3.2.1/rosetta_source/SConscript", line 40, in

scons: warning: No hashlib or MD5 module available, CacheDir() not supported

Post Situation:

## ddg Script Problem

Hi guys. I'm trying to use the ddg script from Sid on an interface, and after changing the DockingProtocol().setup_foldtree to DockingProtocol().set_autofoldtree,
I'm now getting an undefined error for the Interface(dock_jump) step. Is there an equivalent name in 2.0?

-J

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## Pyrosetta 2.0 - Dunbrak library binary not loading - strange repacking score

All,

I am getting large energy increases when repacking a protein using v2.0 of PyRosetta.ScientificLinux64bit (I'm running RHEL5.5_64, Python 2.66)

1st issue On init(), I recieve:

 basic.io.database: Database file opened: .../minirosetta_database/Rama_smooth_dyn.dat_ss_6.4 core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 7533 residue types core.pack.task: Packer task: initialize from command line() Warning: Unable to locate database file Dunbrack02.lib.bin

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## Generate structural fragments

Hello everyone,when I run "/rosetta/fragments/nnmake/make_fragments.pl -nopsipred -nosam -nojufo -noprof -verbose trhl2.fasta",I got the error follow:
[root@localhost input]# /rosetta/fragments/nnmake/make_fragments.pl -nopsipred -nosam -nojufo -noprof -verbose trhl2.fasta
Run options:
be verbose.
don't run psipred.
don't run prof.
don't run jufo.
don't run sam.
FILENAME: trhl2.fasta
no id specified. parse filename instead.
INTERMEDIATE: trhl2.fasta
ID: trhl CHAIN: 2
Warning: can't find executable file /work/chu/src/shareware/psipred/bin/psipred!

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## Dunbrack Library

Hi All;

I'm trying to import a new Dunbrack library into PyRosetta.
I've found the RotamerLibrary class in core.pack.dunbrack._dunbrack_all_at_once and a method create_fa_dunbrack_libraries(), but I am unsure how to call it or setup an instance. Can anyone help? Thanks.

-Jared

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## abinitio - is there a way to limit number of CPU cores the program uses?

So the lab I'm working in has access to a 16 core server but we were told to use no more than 8 cores for any one application. So I was wondering if there is a way to limit the number of cores that abinitio uses while it runs its folding simulations? I looked through the help but didn't see anything that looked like it was what I'm looking for. Thanks for the help.

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## Pyrosetta energy function

I am considering various conformations of a given protein and I should compare their corresponding energy values. I have used Pyrosetta to compute the energies using the "scorefxn = create_score_function('standard')" command. I was under the impression that the PDB structure of a protein should have the minimum energy.

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## Define custom potential?

Is it possible to pull two residues of the same polypeptide chain towards one another during an energy minimization? One way to accomplish this would be to custom design a potential and incorporate this into the scoring function. Is this latter possible?

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## 'DockingProtocol' object has no attribute 'setup_foldtree'

Hi around, sorry for disturbing with my problem that I haven't found posted or solved and if it has been solved I didn't find it. I recently downloaded PyRosetta and would like to use it for docking. The easiest, I thought, is to take an example script that comes with PyRosetta - docking.py, taking the test_dock.pdb that also comes with PyRsoetta and run it to get an idea about computational time. But it doesn't work by writing:
=========
docking.py in ()
15 print "setting up docking fold tree"

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## Problem readin .ccp4 map file

Hi all,
I have bin trying to run the electron_density/molecular_replacement demo at step 4 run_rosetta_mr_nogap.sh and I get the following error. There is nothing wrong with the ccp4 map file (opens fine in other programs)but it appears to be looking for a MRC format map. How do I get the program to accept the ccp4 map?